[Freesurfer] Subcallosal cingulate cortex segmentation/parcellation

[Carlos Alcocer]

External Email - Use Caution

Hi,

I am interested in the aparc+aseg stats for the subcallosal
cinuglate cortex (SCC). When learning freesurfer, the lectures/tutorials
mention not to make manual edits to medial structures which I believe would
include the SCC.

Will the stat output files still be accurate if I don't make edits to these
areas given that the surfaces can look quite messy in those areas at times?

Thank you,

Carlos
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Re: [Freesurfer] FreeSurfer container recipe?

[Bennet Fauber]

External Email - Use Caution

Paul,

That's super helpful and very much appreciated. The template source is
definitely helpful!



On Thu, Apr 6, 2023 at 11:57 AM Wighton, Paul  wrote:
>
> Hi Bennet,
>
> I've been doing my best to support building FreeSurfer containers via 
> neurodocker 
> (https://secure-web.cisco.com/1HCtlZ_46Lc5mEomj3KvdN9SeqbUDClJAUn0DaP42-Jmdbyp1mCHd4Pn6kIwrd4hImk8VOXD8pdbEW12POtXk5HPyMvNnQxSAoP5vx9XaJJmSGC9aX3PkSnL40nNY6DHaHkV9mwZgGoEQeNgIaY_oLpMUJL-kX2Rfwf-lGB4zy2vZ-4pbGm_iCQJ68z95XYjV4xpE90dWdskTq6DWHlyzYs3OTBCSFchJhhALovTp_pCK_4rUeRBXfW72RlVMmWLYZNTEhe2HR6wocWgbTHxXgxtGjTSbru09mFYDCsS1pDz3ocpcwwerw0HqTF8_RtQEwy735EIa2dDums3F4LFVHw/https%3A%2F%2Fgithub.com%2FReproNim%2Fneurodocker).
>
> This template should give you a good idea of the pre-reqs for a FreeSurfer 
> container.
> https://secure-web.cisco.com/1ry5yeGZuLl-9xVuUZw7MASqFRoQ5jitZcduS8Q_TyX8PfdWT4QeXCp90PheZCw0eHYZHapPSe_CA5qKafW6ctRNwlcolk55oq2bXWukiaJQRwIyaat8DOGhqFbtDRLCaRACsaq85D-kUvUr5ukxxHGnoZSvGIddCiv9eyoAzJ56G6AQ1x1SGNWmApKIeMLuj1CiUfuVamJLhJkU7nfWH3Rrt2D3qoatOksOoHMUJL0LaDv8TPX7nU2M1pPIA5YuwAswVsyinG6vtuVKXh6s40MFwuuN09Dzk6LEztzHRK1YwRU2cEKhYiW1WGHBfvdX-s2vyD-H2V_fbHIV-8p_hNQ/https%3A%2F%2Fgithub.com%2FReproNim%2Fneurodocker%2Fblob%2Fmaster%2Fneurodocker%2Ftemplates%2Ffreesurfer.yaml
>
> And you can also use neurodocker to install other required components like 
> FSL, niftyreg, ants, etc.
>
> I also have a PR in the works to support compiling FreeSurfer from source, 
> but it's a mess right now and I haven't had time to clean it up.
> https://secure-web.cisco.com/1s1naXRXHnGUHtOyYiH6kV1qayJ70T7_mmoJdCqzj-28f-h_0o4QP4rhXdQnBCVMfybvU5stQ7ju7c04JmdpM9riBZ-pxwyrDxZGslwKD5a_N2mN0M_s6vp_XtpTigTFFRQ5TmF7RR-JomSTIpfoobfyfkEyK67EdRXwUfyWw9dTwIVII8sBE8R2Y8ZKm25c03ORibIGH5pmAHKa2E1wx4G9CGy81mHKc6sA9yvtpYqW7vMPNYTLmDi09uRFc5-ABGFNYTQmZR9HlBtm4b9S-s0IKpxvKFb4Hc50i2KKRzWAMTRreXR11MY-qzRi83OMRlmDGl7heK30GC9y2UVNXsw/https%3A%2F%2Fgithub.com%2FReproNim%2Fneurodocker%2Fpull%2F445
>
> Hope this helps,
>
> -Paul
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bennet Fauber 
> 
> Sent: Thursday, April 6, 2023 7:34 AM
> To: Freesurfer support list
> Subject: [Freesurfer] FreeSurfer container recipe?
>
> External Email - Use Caution
>
> In reply to mail from Mitchell Horn, Douglas Greve replied
>
> > The math libraries changed between 7 and 8, nothing we can do about it. 
> > When I
> > have to run things on a centos8 machine, I generally run in a centos7 
> > singularity
> > container (which we might be able to make available, without support:)
>
> Would it be possible to get just the Singularity definition file for
> the CentOS 7 Singularity image that you use posted to the FS wiki?
>
> We're happy to do the building, but having a file that lists the
> needed prerequisites that need to be installed via yum prior to
> installing FreeSurfer would be very helpful.  It would also help to
> see how you handle the needed FSL components, and I think at least
> some portion of ANTs is needed for TRACULA, so even just which
> binaries are needed would be a help, too..
>
> Thanks for considering this request, which I hope is not as burdensome
> as providing the fully built container.
>
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>
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Re: [Freesurfer] FreeSurfer container recipe?

[Wighton, Paul]

Hi Bennet,

I've been doing my best to support building FreeSurfer containers via 
neurodocker (https://github.com/ReproNim/neurodocker).

This template should give you a good idea of the pre-reqs for a FreeSurfer 
container.
https://github.com/ReproNim/neurodocker/blob/master/neurodocker/templates/freesurfer.yaml

And you can also use neurodocker to install other required components like FSL, 
niftyreg, ants, etc.

I also have a PR in the works to support compiling FreeSurfer from source, but 
it's a mess right now and I haven't had time to clean it up.
https://github.com/ReproNim/neurodocker/pull/445

Hope this helps,

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bennet Fauber 

Sent: Thursday, April 6, 2023 7:34 AM
To: Freesurfer support list
Subject: [Freesurfer] FreeSurfer container recipe?

External Email - Use Caution

In reply to mail from Mitchell Horn, Douglas Greve replied

> The math libraries changed between 7 and 8, nothing we can do about it. When I
> have to run things on a centos8 machine, I generally run in a centos7 
> singularity
> container (which we might be able to make available, without support:)

Would it be possible to get just the Singularity definition file for
the CentOS 7 Singularity image that you use posted to the FS wiki?

We're happy to do the building, but having a file that lists the
needed prerequisites that need to be installed via yum prior to
installing FreeSurfer would be very helpful.  It would also help to
see how you handle the needed FSL components, and I think at least
some portion of ANTs is needed for TRACULA, so even just which
binaries are needed would be a help, too..

Thanks for considering this request, which I hope is not as burdensome
as providing the fully built container.

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contains patient information, please contact the Mass General Brigham 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] -gcareg dropped from -autorecon2-volonly

[Douglas N. Greve]

ah, I see. OK, I've fixed this in dev.

On 4/4/2023 4:59 PM, Christopher Markiewicz wrote:
>  External Email - Use Caution
>
> Hi Doug,
>
> Sorry for the delay. CAReg shows up, but not GCAReg:
>
> $ grep -A6 "case .-autorecon2-volonly" $FREESURFER_HOME/bin/recon-all
>  case "-autorecon2-volonly":
>set DoRemoveNeck = 0;
>set DoSkullLTA   = 0;
>set DoSegStats   = 0;
>set DoCANormalize= 1;
>set DoCAReg  = 1;
>set DoCALabel= 1;
>
> Best,
> Chris
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N. Greve 
> 
> Sent: Thursday, March 30, 2023 09:29
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] -gcareg dropped from -autorecon2-volonly
>
> In my version, it appears just after DoCANormalize. Can you have grep
> print out one more line?
>
> On 3/28/2023 9:05 AM, Christopher Markiewicz wrote:
>>   External Email - Use Caution
>>
>> Hi Doug,
>>
>> $ cat $FREESURFER_HOME/build-stamp.txt
>> freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
>> $ grep -A4 "case .-autorecon2-volonly" $FREESURFER_HOME/bin/recon-all
>>   case "-autorecon2-volonly":
>> set DoRemoveNeck = 0;
>> set DoSkullLTA   = 0;
>> set DoSegStats   = 0;
>> set DoCANormalize= 1;
>>
>> I'm also not seeing it in `dev` on GitHub: 
>> https://secure-web.cisco.com/19BPC0I5kosNy_-RSRAWv0WGSAh5adNjGaAo84dO6_vclc0xTDdaWDhzjw4v7ppIcDpDNswchLRbpmE36ysQBkiSWjw92p1HKyrkhU-0zbtFv4PraKshl7lT1z-a16c9dB0tN4yZo_820XxuOeTrje-GYr8LsSd--qY_M5HRd1G6fSraiGRRAops64STReDvpoi0BXA-zlhMdnAhELxhrvob5NlWaNnWqeDe6wSEbT-hxMaP2uo-Bt_piurh13j7769MK9sNR0k-7Y9JyehZM_3gicUwLa4OuBnJ0Y_Ciig6EqP4woHYnsEIVljYRyK8kXmAy_9umFAvwvA9MpVIJmg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fscripts%2Frecon-all%23L7020-L7031
>>
>> Best,
>> Chris
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N. Greve 
>> 
>> Sent: Monday, March 27, 2023 11:16
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] -gcareg dropped from -autorecon2-volonly
>>
>> In 7.2 it appears to be there (and in 7.3 and in dev and in 7.0 and 7.1)
>>
>>case "-autorecon2-volonly":
>>  set DoGCAReg = 1;
>>  set DoRemoveNeck = 0;
>>  set DoSkullLTA   = 0;
>>  set DoCANormalize= 1;
>>  set DoCAReg  = 1;
>>  set DoCALabel= 1;
>>  set DoSegStats   = 0;
>>  set DoNormalization2 = 1;
>>  set DoMaskBFS= 1;
>>  set DoSegmentation   = 1;
>>  set DoFill   = 1;
>>  breaksw
>>
>>
>> On 3/24/2023 9:57 AM, Christopher Markiewicz wrote:
>>>External Email - Use Caution
>>>
>>> Hi all,
>>>
>>> This is a duplicate of a bug report on GitHub 
>>> (https://secure-web.cisco.com/1C5EnDIMtZh6wk0SJMqe8l166ycKmSdnL5atT3CIHDPAY15Ixtf93Rif0FmPFCZaftXbqlhK5AbXT22OXXCJq9JgIiSOyglr8IF1n3lOAzrtCIHcr8C2aLwqsXcMciJwp9Mz2DV4vmcWjm2v_xTUmw6hoea4u37a4hkUyIkSRKIBbOEC9mKcGdJ41Nbz86rmDYbEm3v5pV6zuR3zISglz0_aPe4hJhmj_y7BHipJWdwr3J3pwKPc5BT5WbnmtOEJ6hBkSswM8xHN-3ZfID-bPa2VEltISdFH8ITDhpQJKlPlhEYwtkSxcoWugX9kNCGiWbWsbTqR4PbpJPvp4qp4e5w/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F1081):
>>>
>>> `DoGCAReg` was removed from `-autorecon2-volonly` in commit 
>>> 4b9af5fc8c559e944400b885ef89f3682f94e0da, but this seems unrelated to the 
>>> commit message. It's still in `-autorecon2`. Is there a reason it shouldn't 
>>> be present, or was this a mistake?
>>>
>>> This issue affects versions 7.3.0+. Apologies for doubling up if you saw 
>>> it; my impression is the mailing list is more actively monitored.
>>>
>>> Best,
>>> Chris
>>>
>>> ___
>>> Freesurfer mailing list
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>> ___
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>> The information in this 

[Freesurfer] Open research assistant position at Ohio State University

[Osher, David E.]

External Email - Use Caution

The Cognition and Brain Circuitry Laboratory at the Ohio State University is 
recruiting a research assistant. Primary duties include: conducting 
neuroscience research on the functional and structural architecture of the 
human brain, and its role in cognition; programming, running, and analyzing 
behavioral and brain-imaging experiments using functional magnetic resonance 
imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and 
behavioral assessments; scoring and coding data; performing statistical 
analyses using programs such as, MATLAB, Python, and shell scripting; 
recruiting research participants; maintaining participant databases; developing 
outreach letters. The position is available for one year with the possibility 
of extension based on satisfactory performance and availability of funds.

Required qualifications include: Bachelor's degree in psychology, neuroscience, 
cognitive science, computer science, data science, engineering, physics, or 
math; conduct of social science research is required; experience in a social 
science research capacity.
Highly desired: strong mathematical, statistical, and coding skills (e.g., 
MATLAB, Python, shell scripting); strong interpersonal skills for interacting 
with a diverse group of people; strong organizational skills.

This position is an excellent opportunity for individuals considering future 
graduate studies in cognitive and computational neuroscience (every one of our 
research assistants has successfully been admitted into doctoral programs!). We 
are seeking an aspiring, self-motivated researcher with strong 
coding/programming skills who is excited about the brain, cognitive 
neuroscience, and/or clinical disorders and demonstrates evidence of a serious 
interest in a career in the field.

If you are interested in being considered for these positions, please apply 
online at 
https://secure-web.cisco.com/1TciY0h9Hnogs0Vsz6IpkMg3S9JvHoraefFGDv9JWfB8mvIlucAJE9ulGkry9qT63OAfHCsMqIHsNzfSzcIxL8Cno70feKG9mJSeN07E5Tn8_y_wEQZxjZ9pgg_wrYvSGwz9KoiCbxloxQVszrBBAZfVAR7QAxd0j8LhEJczk8XTNEMPcvGzragjXAcnFTD_qlS4a1051SmwqsyqyejO0swGCLxb_jjBsniLSjp6EzD3R48dWcfU1M4WjF9NaL8Ix16ocyO9iYKZeI7DphPZ9imurfC1pHxqkSOXO-Xc2HLAvgc4cTZtiFK57N31SidMXKMAO3uxBHq_qEAsG_2veFw/https%3A%2F%2Fosu.wd1.myworkdayjobs.com%2Fen-US%2FOSUCareers%2Fjob%2FResearch-Senior-Technician_R74514-1
 and submit a current CV and names of three references.


If you have questions about the position or the lab, please contact Dr. David 
Osher at oshe...@osu.edu

The Ohio State University is an equal opportunity employer. All qualified 
applicants will receive consideration for employment without regard to race, 
color, religion, sex, sexual orientation or identity, national origin, 
disability status, or protected veteran status.


_
David E. Osher, Ph.D.
Assistant Professor of Psychology
The Ohio State University
davidosher.com
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Re: [Freesurfer] mri_glmfit correction across lobes

[Douglas N. Greve]

You can, but you need to give mri_glmfit the specific label to use as a 
mask (eg, --label or --mask). You can extract labels from an annot with 
mri_annotation2label. Then mri_glmfit-sim will automatically restrict 
the correction to that label


On 4/6/2023 10:05 AM, John Anderson wrote:


External Email - Use Caution

Dear Dr Greve,
Apologize for not providing a clear explanation earlier. The file 
lh.all.suvr.sm05.proj0.5.nii.gz is the result of combining all SUVR 
maps, using mri_concat, after projecting them onto the brain surface 
with mri_vol2surf.
I would like to know if it is possible to use mri_glmfit-sim to 
correct for specific regions of interest (such as lobes) instead of 
correcting the entire brain.
I am using the following command: mri_glmfit-sim --glmdir 
lh.suvr.glmdir --cache 4 pos --cwp 0.05 --2spaces


When I include the "--annot lobes" option in my command 
(mri_glmfit-sim --glmdir lh.suvr.glmdir --cache 4 pos --cwp 0.05 
--2spaces --annot lobes), the resulting statistical output is similar, 
but the annotations are replaced with their corresponding lobes. 
However, p-values are not adjusted for the number of regions of 
interest specified in the "--annot" option. Thanks again


On Wed, Apr 5, 2023 at 10:46 PM Douglas N. Greve 
 wrote:


What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from?
The name looks like it might be a voxel-wise map, but you say
something about ROIs. mri_glmfit does not correct for multiple
comparisons. For ROI-based analyses, you can use bonferroni or
FDR. For maps you can use mri_glmfit-sim.

On 4/4/2023 4:53 PM, John Anderson wrote:


External Email - Use Caution

Hello Freesurfer,
Currently, I am using the Petsurfer manual, which is easily
understandable and clear. Nonetheless, I have a question
regarding the "mri_glmfit" step.
As far as I know, this command is used to correct data for
multiple comparisons among all the ROIs in the aparc+aseg.mgz
file. Can you please confirm if my understanding is correct?

mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd
2G0C.fsgd --C patients_vs_controls.mtx --surf fsaverage lh
--cortex --glmdir lh.patinets_vs_controls

In particular, I am interested in correcting data across lobes
instead of across all ROIs. I followed the steps mentioned in the
FS forum to create lobes, and I can observe lobe annotations in
the wmparc.mgz file. I am curious to know whether using the
"--annot" flag will adjust the p-values across different lobe
ROIs instead of all ROIs in the aparc+aseg.mgz file. I have
attempted this, but it appears to only change the name of the
annotation in the final statistics file, and the p-value remains
the same. Do I need to include any additional arguments in the
command?

Thanks for your help
John

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Re: [Freesurfer] mri_glmfit correction across lobes

[John Anderson]

External Email - Use Caution

Dear Dr Greve,
Apologize for not providing a clear explanation earlier. The file
lh.all.suvr.sm05.proj0.5.nii.gz is the result of combining all SUVR maps,
using mri_concat, after projecting them onto the brain surface with
mri_vol2surf.
I would like to know if it is possible to use mri_glmfit-sim to correct for
specific regions of interest (such as lobes) instead of correcting the
entire brain.
I am using the following command: mri_glmfit-sim --glmdir lh.suvr.glmdir
--cache 4 pos --cwp 0.05 --2spaces

When I include the "--annot lobes" option in my command (mri_glmfit-sim
--glmdir lh.suvr.glmdir --cache 4 pos --cwp 0.05 --2spaces --annot lobes),
the resulting statistical output is similar, but the annotations are
replaced with their corresponding lobes. However, p-values are not adjusted
for the number of regions of interest specified in the "--annot" option.
Thanks again

On Wed, Apr 5, 2023 at 10:46 PM Douglas N. Greve 
wrote:

> What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from? The name
> looks like it might be a voxel-wise map, but you say something about ROIs.
> mri_glmfit does not correct for multiple comparisons. For ROI-based
> analyses, you can use bonferroni or FDR. For maps you can use
> mri_glmfit-sim.
>
> On 4/4/2023 4:53 PM, John Anderson wrote:
>
> External Email - Use Caution
> Hello Freesurfer,
> Currently, I am using the Petsurfer manual, which is easily understandable
> and clear. Nonetheless, I have a question regarding the "mri_glmfit" step.
> As far as I know, this command is used to correct data for multiple
> comparisons among all the ROIs in the aparc+aseg.mgz file. Can you please
> confirm if my understanding is correct?
>
> mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd 2G0C.fsgd --C
> patients_vs_controls.mtx --surf fsaverage lh --cortex --glmdir
> lh.patinets_vs_controls
>
> In particular, I am interested in correcting data across lobes instead of
> across all ROIs. I followed the steps mentioned in the FS forum to create
> lobes, and I can observe lobe annotations in the wmparc.mgz file. I am
> curious to know whether using the "--annot" flag will adjust the p-values
> across different lobe ROIs instead of all ROIs in the aparc+aseg.mgz file.
> I have attempted this, but it appears to only change the name of the
> annotation in the final statistics file, and the p-value remains the same.
> Do I need to include any additional arguments in the command?
>
> Thanks for your help
> John
>
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[Freesurfer] FreeSurfer container recipe?

[Bennet Fauber]

External Email - Use Caution

In reply to mail from Mitchell Horn, Douglas Greve replied

> The math libraries changed between 7 and 8, nothing we can do about it. When I
> have to run things on a centos8 machine, I generally run in a centos7 
> singularity
> container (which we might be able to make available, without support:)

Would it be possible to get just the Singularity definition file for
the CentOS 7 Singularity image that you use posted to the FS wiki?

We're happy to do the building, but having a file that lists the
needed prerequisites that need to be installed via yum prior to
installing FreeSurfer would be very helpful.  It would also help to
see how you handle the needed FSL components, and I think at least
some portion of ANTs is needed for TRACULA, so even just which
binaries are needed would be a help, too..

Thanks for considering this request, which I hope is not as burdensome
as providing the fully built container.

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